Differential transcriptome analysis of the common shrimp Crangon crangon: Special focus on the nuclear receptors and RNAi-related genes

Christiaens, Olivier; Delbare, D.; Neste, Christophe Van; Cappelle, Kaat; Yu, Na; Wilde, Ruben De; Nieuwerburgh, Filip Van; Deforce, Dieter; Cooreman, Kris; Smagghe, Guy

doi:10.1016/j.ygcen.2014.06.016

Cited by 19 publications

(12 citation statements)

References 56 publications

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“…The authors speculate that Loquacious, a similar protein normally associated to the miRNA pathway, could take over the role of R2D2 in these basal insect species. This assumption, which was already suggested by Christiaens et al (2015) and Taning et al (2016a) is also supported by reports of Loquacious being functional as cofactor to Dicer-2 in the siRNA pathway in D. melanogaster (Czech et al, 2008;Marques et al, 2010;Okamura et al, 2008). In Crustacea, another protein has been identified as a cofactor for Dicer-2, namely an orthologue of the transactivating response (TAR) RNA binding protein (TRBP) (Lai and Aboobaker, 2017).…”

Section: Rnai Machinery Genes Repertoiresupporting

confidence: 56%

“…However, no further studies have been conducted to elucidate the role of this extra Dicer protein. Furthermore, in other crustacean species in which the RNAi pathways were investigated, such as the brown shrimp C. crangon, the black tiger shrimp P. monodon and the Pacific white shrimp L. vannamei, only two Dicers were found (Chen et al, 2011a;Christiaens et al, 2015;Li et al, 2013;Su et al, 2008;Yao et al, 2010). In ticks and mites (Acari), a variable number of Dicers was reported as well.…”

Section: Rnai Machinery Genes Repertoirementioning

confidence: 99%

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Literature review of baseline information on RNAi to support the environmental risk assessment of RNAi‐based GM plants

Christiaens

Dzhambazova

Kostov

et al. 2018

EFS3

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This report is the outcome of an EFSA procurement (OC/EFSA/GMO/2015/02) which aims at reviewing relevant scientific information on RNA interference (RNAi) that could serve as baseline information for the environmental risk assessment of RNAi‐based genetically modified (GM) plants. The report is based on a systematic literature search on the use of RNAi molecules in arthropods, nematodes, annelids and molluscs with dsRNA, siRNA and miRNA applied primarily through feeding and soaking (oral ingestion). The numbers of retrieved publications covering these areas are reported, along with the species name, life stages tested, the target gene and its function, details of the test substances and their concentrations used, methods of delivery and effects. Separate sections discuss the available information on: (1) the uptake and systematic spread of RNAi activity, including a description of the various components involved in this process; (2) the mechanisms of dsRNA‐, siRNA‐ and miRNA‐elicited gene silencing and the different factors involved in RNAi efficiency; (3) routes of exposure of the biotic and abiotic environment to dsRNA, siRNA and miRNA from GM plants; (4) the environmental fate of dsRNA, siRNA and miRNA; and (5) the various factors that may limit non‐target effects including exposure, factors influencing the silencing efficiency of dsRNA, siRNA and miRNA, possible unintended and off‐target effects, and their mechanisms. Finally, an overview of the species of arthropods, nematodes, annelids and molluscs for which genomic data are available is also presented. The report identifies some of the challenges involved in developing plants with RNAi systems which affect invertebrate gene expression. The report also concludes that, currently, knowledge on issues such as exposure, specificity, offtarget effects, sequence similarities and bioinformatics is very limited, as only a few RNAi expressing plants which specifically target invertebrate species have been developed and comprehensively studied.

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Section: Rnai Machinery Genes Repertoiresupporting

confidence: 56%

Section: Rnai Machinery Genes Repertoirementioning

confidence: 99%

Literature review of baseline information on RNAi to support the environmental risk assessment of RNAi‐based GM plants

Christiaens

Dzhambazova

Kostov

et al. 2018

EFS3

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“…Transcriptomics using NGS technology has revealed genes involved in stress response, reproduction, development, molting and growth, limb regeneration, immune response, endocrinology, and nutrition and digestion in decapod crustaceans (Sagi et al 2013; Tom et al 2013; Durica et al 2014; Ghaffari et al 2014; Hao et al 2014; Lv et al, 2014, 2015; Shen et al 2014; Song et al 2014; Tom et al 2014; Wei et al 2014a, 2014b; Abehsera et al 2015; Chandler et al 2015; Christiaens et al 2015; Huang et al 2015; Johnson et al 2015; Li et al 2015a, 2015b; Ventura et al 2014, 2015; Verbruggen et al 2015; Wang et al 2015; Das et al 2016a). It is clear from the input received at the SICB meeting and the ten symposium papers in this issue (Armstrong and Stillman 2016; Chandler et al 2016; Clark and Greenwood 2016; Das and Mykles 2016; Das et al 2016b; Havird and Santos 2016a, 2016b; Johnson et al 2016; Powell et al 2016; Tarrant et al 2016) that a greater understanding of the relationship between transcriptomic and phenotypic change in decapod crustaceans will not be achieved until more powerful and applicable “-omic” tools and resources are developed.…”

Section: Future Directions and Recommendationsmentioning

confidence: 99%

Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology

Mykles

Burnett

Durica

et al. 2016

Integr. Comp. Biol.

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High-throughput RNA sequencing (RNA-seq) technology has become an important tool for studying physiological responses of organisms to changes in their environment. De novo assembly of RNA-seq data has allowed researchers to create a comprehensive catalog of genes expressed in a tissue and to quantify their expression without a complete genome sequence. The contributions from the “Tapping the Power of Crustacean Transcriptomics to Address Grand Challenges in Comparative Biology” symposium in this issue show the successes and limitations of using RNA-seq in the study of crustaceans. In conjunction with the symposium, the Animal Genome to Phenome Research Coordination Network collated comments from participants at the meeting regarding the challenges encountered when using transcriptomics in their research. Input came from novices and experts ranging from graduate students to principal investigators. Many were unaware of the bioinformatics analysis resources currently available on the CyVerse platform. Our analysis of community responses led to three recommendations for advancing the field: (1) integration of genomic and RNA-seq sequence assemblies for crustacean gene annotation and comparative expression; (2) development of methodologies for the functional analysis of genes; and (3) information and training exchange among laboratories for transmission of best practices. The field lacks the methods for manipulating tissue-specific gene expression. The decapod crustacean research community should consider the cherry shrimp, Neocaridina denticulata, as a decapod model for the application of transgenic tools for functional genomics. This would require a multi-investigator effort.

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“…Fifteen genes related to the RISC complex and four genes involved in dsRNA uptake were also identified in C. Crangon , including FBX011 , SR‐C , Sid‐1A and Sid‐1B (Christiaens et al . ). This transcriptome analysis revealed a set of RNAi core genes that is similar to that which is present in most insect species.…”

Section: Molecular Mechanismmentioning

confidence: 97%

“…The above studies have proven the presence of genes related to the RNAi machinery in shrimp. However, the information on these RNAi-related genes was still fragmentary, until Christiaens et al (2015) made a major step in providing an overview of a large number of RNAi-related genes in Crangon crangon through a transcriptome analysis and annotation of all RNAi-related transcripts. Core machinery genes from the three main RNAi pathways were identified, including Dicer-1, Ago-1, drosha, Pasha and Loquacious gene for the miRNA pathway, Dicer-2, Ago-2A and Ago-2B for the siRNA pathway, and Piwi1, Piwi2 and Ago-3 genes for the piRNA pathway.…”

Section: Molecular Mechanismmentioning

confidence: 99%

RNA interference in shrimp and potential applications in aquaculture

Nguyen

Christiaens

Bossier

et al. 2016

Reviews in Aquaculture

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As the RNA interference mechanism was discovered, researchers have made huge strides in unravelling biological mechanisms at the gene level in a wide range of organisms. RNAi is a simple and rapid method that allows silencing gene expression at the post-transcriptional level and is triggered by the introduction of double-stranded RNA into the cell, leading to the degradation of the corresponding mRNA. In this review, we will provide an overview of successful RNAi experiments to date in Crustacea, and shrimp in particular, with special focus on various potential applications of RNA interference in research and aquaculture. An important aspect of RNAi in any species is the delivery of the double-stranded RNA and the barriers that have to be overcome to get the dsRNA into the target cells. Different options, experimental procedures, success rates and challenges in using RNAi are discussed in this review

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Differential transcriptome analysis of the common shrimp Crangon crangon: Special focus on the nuclear receptors and RNAi-related genes

Cited by 19 publications

References 56 publications

Literature review of baseline information on RNAi to support the environmental risk assessment of RNAi‐based GM plants

Literature review of baseline information on RNAi to support the environmental risk assessment of RNAi‐based GM plants

Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology

RNA interference in shrimp and potential applications in aquaculture

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